Mercurial > repos > iuc > pcdl_plot_timeseries

annotate pcdl_plot_timeseries.xml @ 0:c8c9631bec71 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
author iuc
date Mon, 04 Aug 2025 19:00:59 +0000
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0
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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1 <tool id="pcdl_plot_timeseries" name="pcdl_plot_timeseries" version="3.0.1+galaxy0" profile="21.05">
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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2 <macros>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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3 <import>pcdl_macros.xml</import>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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4 </macros>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
iuc
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5 <requirements>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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6 <expand macro="requirement"/>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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7 </requirements>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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8 <command><![CDATA[
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9 #import re
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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10 mkdir output_pc &&
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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11 #for $file in $path:
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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12 #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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13 ln -s '$file' output_pc/$filename &&
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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14 #end for
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15
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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16 pcdl_plot_timeseries output_pc '$focus_cat' '$focus_num' '$aggregate_num'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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17 --custom_data_type $custom_data_type
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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18 --microenv $microenv
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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19 --physiboss $physiboss
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20 --settingxml 'none'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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21 --verbose $verbose
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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22 --frame $frame
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23 --z_slice '$z_slice'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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24 --logy $logy
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25 --ylim '$ylim'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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26 --secondary_y $secondary_y
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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27 --subplots $subplots
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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28 --sharex $sharex
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29 --sharey $sharey
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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30 --linestyle $linestyle
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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31 --linewidth '$linewidth'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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32 --cmap '$cmap'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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33 --color '$color'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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34 --grid $grid
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35 --legend $legend
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36 --yunit '$yunit'
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37 --title '$title'
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38 --figsizepx $figsizepx_x $figsizepx_y
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39 --ext $ext
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40 --figbgcolor '$figbgcolor'
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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41 ]]></command>
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42 <inputs>
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43 <section name="essential" title="essential:" expanded="true">
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44 <expand macro="path"/>
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45 <expand macro="focus_cat"/>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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46 <expand macro="focus_num"/>
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47 <expand macro="aggregate_num"/>
c8c9631bec71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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48 <expand macro="custom_data_type"/>
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49 <expand macro="frame"/>
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50 <expand macro="z_slice"/>
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51 <expand macro="logy"/>
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52 <expand macro="ylim"/>
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53 <expand macro="secondary_y"/>
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54 <expand macro="subplots"/>
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55 <expand macro="sharex"/>
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56 <expand macro="sharey"/>
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57 <expand macro="linestyle"/>
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58 <expand macro="linewidth"/>
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59 <expand macro="cmap"/>
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60 <expand macro="color"/>
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61 <expand macro="grid"/>
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62 <expand macro="legend"/>
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63 <expand macro="yunit"/>
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64 <expand macro="title"/>
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65 <expand macro="figsizepx_x"/>
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66 <expand macro="figsizepx_y"/>
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67 <expand macro="ext"/>
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68 <expand macro="figbgcolor"/>
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69 </section>
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70 <section name="advanced" title="advanced:" expanded="false">
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71 <expand macro="microenv"/>
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72 <expand macro="physiboss"/>
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73 <expand macro="verbose"/>
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74 </section>
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75 </inputs>
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76 <outputs>
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77 <collection name="timeseries_plot" type="list">
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78 <discover_datasets pattern="(?P&lt;designation&gt;timeseries_.+)\.jpeg" format="jpg" directory="output_pc" visible="false"/>
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79 </collection>
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80 </outputs>
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81 <tests>
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82 <test expect_num_outputs="1">
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83 <section name="essential">
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84 <param name="path">
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85 <expand macro="output"/>
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86 </param>
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87 </section>
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88 <section name="advanced">
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89 <param name="verbose" value="true"/>
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90 </section>
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91 <output_collection name="timeseries_plot" count="1">
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92 <element name="timeseries_cell_total_count">
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93 <assert_contents>
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94 <has_text text="JFIF"/>
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95 </assert_contents>
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96 </element>
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97 </output_collection>
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101 This function to generate a timeseries plot and either returns a matplotlib figure or an image file (jpeg, png, tiff).
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102
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103 Homepage: https://github.com/elmbeech/physicelldataloader
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104 ]]></help>
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105 <citations>
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106 <expand macro="citation"/>
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107 </citations>
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108 </tool>